Iron in PDB 3wsd: Oxidized Hcgd From Methanocaldococcus Jannaschii

The structure of Oxidized Hcgd From Methanocaldococcus Jannaschii, PDB code: 3wsd was solved by T.Fujishiro, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.67 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.260, 136.150, 160.850, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.4

The structure of Oxidized Hcgd From Methanocaldococcus Jannaschii also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Oxidized Hcgd From Methanocaldococcus Jannaschii (pdb code 3wsd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Oxidized Hcgd From Methanocaldococcus Jannaschii, PDB code: 3wsd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:39.6 occ:1.00 NE2 A:HIS71 2.0 43.1 1.0 NE2 A:HIS221 2.1 39.1 1.0 OE1 A:GLU225 2.4 42.8 1.0 CE1 A:HIS221 2.9 36.5 1.0 CL A:CL303 2.9 50.3 1.0 CE1 A:HIS71 3.0 41.1 1.0 CD A:GLU225 3.1 44.4 1.0 CD2 A:HIS71 3.1 41.2 1.0 OE2 A:GLU225 3.1 49.2 1.0 CD2 A:HIS221 3.2 35.0 1.0 O A:HOH444 3.5 44.6 1.0 FE A:FE302 3.8 45.0 0.4 ND1 A:HIS221 4.0 34.5 1.0 ND1 A:HIS71 4.1 39.9 1.0 CG A:HIS71 4.2 37.7 1.0 CG A:HIS221 4.2 35.4 1.0 CA A:GLY178 4.3 31.7 1.0 CD2 A:HIS70 4.3 27.4 1.0 NE2 A:HIS103 4.4 43.1 1.0 CG A:GLU225 4.4 41.5 1.0 NE2 F:HIS204 4.4 51.2 1.0 NE2 A:HIS70 4.4 31.0 1.0 CE1 F:HIS204 4.6 55.6 1.0 N A:TYR179 4.7 34.3 1.0

Iron binding site 2 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:45.0 occ:0.44 OE2 A:GLU225 2.2 49.2 1.0 OD1 A:ASP107 2.5 47.2 1.0 NE2 A:HIS70 2.5 31.0 1.0 OD2 A:ASP107 2.5 45.9 1.0 CG A:ASP107 2.8 43.8 1.0 O A:HOH444 3.3 44.6 1.0 CE1 A:HIS70 3.3 29.4 1.0 CD A:GLU225 3.4 44.4 1.0 CD2 A:HIS70 3.6 27.4 1.0 FE A:FE301 3.8 39.6 1.0 O A:SER177 3.9 30.4 1.0 O A:HOH425 4.1 35.0 1.0 OE1 A:GLU225 4.1 42.8 1.0 NE2 A:HIS103 4.2 43.1 1.0 CD2 A:HIS103 4.2 41.8 1.0 CB A:ASP107 4.3 37.9 1.0 CD1 A:LEU113 4.4 31.3 1.0 ND1 A:HIS70 4.5 28.8 1.0 CG A:GLU225 4.5 41.5 1.0 OG A:SER177 4.5 32.0 1.0 CL A:CL303 4.7 50.3 1.0 CG A:HIS70 4.7 27.4 1.0 C A:SER177 4.7 28.5 1.0 NE2 A:HIS71 4.9 43.1 1.0 CA A:GLY178 5.0 31.7 1.0

Iron binding site 3 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:66.7 occ:0.58 OE1 B:GLU225 2.1 52.0 1.0 OD1 B:ASP107 2.5 45.4 1.0 OD2 B:ASP107 2.6 41.0 1.0 NE2 B:HIS70 2.7 34.2 1.0 CG B:ASP107 2.9 38.1 1.0 CD B:GLU225 3.3 48.0 1.0 O B:HOH436 3.3 42.0 1.0 CE1 B:HIS70 3.5 30.9 1.0 O B:SER177 3.7 41.3 1.0 CD2 B:HIS70 3.7 29.9 1.0 FE B:FE302 3.7 72.7 1.0 OE2 B:GLU225 4.0 49.1 1.0 O B:HOH411 4.1 36.3 1.0 NE2 B:HIS103 4.2 37.2 1.0 CD2 B:HIS103 4.2 34.3 1.0 CB B:ASP107 4.3 30.2 1.0 CG B:GLU225 4.4 42.9 1.0 CL B:CL303 4.5 47.7 1.0 OG B:SER177 4.5 45.0 1.0 C B:SER177 4.5 35.3 1.0 CD1 B:LEU113 4.5 29.5 1.0 ND1 B:HIS70 4.7 29.1 1.0 CA B:GLY178 4.8 32.1 1.0 CG B:HIS70 4.8 28.1 1.0 NE2 B:HIS71 5.0 49.0 1.0 N B:GLY178 5.0 30.3 1.0

Iron binding site 4 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:72.7 occ:1.00 NE2 B:HIS71 2.1 49.0 1.0 NE2 B:HIS221 2.2 34.3 1.0 OE2 B:GLU225 2.3 49.1 1.0 CL B:CL303 2.8 47.7 1.0 CD B:GLU225 2.9 48.0 1.0 CE1 B:HIS221 2.9 30.9 1.0 OE1 B:GLU225 3.0 52.0 1.0 CE1 B:HIS71 3.0 42.9 1.0 CD2 B:HIS71 3.2 42.2 1.0 CD2 B:HIS221 3.3 31.4 1.0 FE B:FE301 3.7 66.7 0.6 O B:HOH436 4.0 42.0 1.0 ND1 B:HIS221 4.1 31.2 1.0 ND1 B:HIS71 4.1 41.0 1.0 CA B:GLY178 4.2 32.1 1.0 CG B:HIS71 4.3 39.6 1.0 CD2 B:HIS70 4.3 29.9 1.0 CG B:GLU225 4.3 42.9 1.0 CG B:HIS221 4.3 31.1 1.0 NE2 B:HIS103 4.3 37.2 1.0 CE1 D:HIS204 4.4 47.2 1.0 NE2 B:HIS70 4.4 34.2 1.0 NE2 D:HIS204 4.5 46.9 1.0 N B:TYR179 4.8 39.9 1.0 CD2 B:HIS103 5.0 34.3 1.0 C B:GLY178 5.0 35.2 1.0

Iron binding site 5 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:44.1 occ:0.41 OE1 C:GLU225 2.0 49.5 1.0 NE2 C:HIS70 2.2 43.5 1.0 OD1 C:ASP107 2.5 60.5 1.0 OD2 C:ASP107 2.7 56.9 1.0 CG C:ASP107 2.9 54.4 1.0 CE1 C:HIS70 3.1 41.1 1.0 CD C:GLU225 3.2 46.1 1.0 CD2 C:HIS70 3.3 43.3 1.0 FE C:FE302 3.6 47.3 1.0 OE2 C:GLU225 3.8 47.6 1.0 O C:SER177 4.0 48.8 1.0 CD2 C:HIS103 4.1 42.3 1.0 NE2 C:HIS103 4.2 45.8 1.0 ND1 C:HIS70 4.3 38.4 1.0 CD1 C:LEU113 4.3 29.3 1.0 CG C:GLU225 4.3 43.6 1.0 CG C:HIS70 4.4 40.3 1.0 CB C:ASP107 4.4 45.7 1.0 OG C:SER177 4.6 46.8 1.0 O C:HOH411 4.6 35.4 1.0 C C:SER177 4.7 40.9 1.0 CL C:CL303 4.8 48.2 1.0 CA C:GLY178 4.9 30.7 1.0 NE2 C:HIS71 4.9 51.5 1.0 O C:HIS103 4.9 37.6 1.0

Iron binding site 6 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:47.3 occ:1.00 OE2 C:GLU225 2.2 47.6 1.0 NE2 C:HIS71 2.2 51.5 1.0 NE2 C:HIS221 2.3 34.7 1.0 CD C:GLU225 2.8 46.1 1.0 OE1 C:GLU225 2.8 49.5 1.0 CL C:CL303 3.0 48.2 1.0 CE1 C:HIS221 3.0 36.6 1.0 CE1 C:HIS71 3.0 46.4 1.0 CD2 C:HIS71 3.3 46.9 1.0 CD2 C:HIS221 3.4 33.9 1.0 FE C:FE301 3.6 44.1 0.4 CD2 C:HIS70 4.1 43.3 1.0 ND1 C:HIS221 4.2 37.5 1.0 CG C:GLU225 4.2 43.6 1.0 NE2 C:HIS70 4.2 43.5 1.0 ND1 C:HIS71 4.2 42.8 1.0 CA C:GLY178 4.2 30.7 1.0 CG C:HIS221 4.3 35.6 1.0 CG C:HIS71 4.4 40.4 1.0 NE2 C:HIS103 4.4 45.8 1.0 NE2 E:HIS204 4.6 51.0 1.0 CE1 E:HIS204 4.6 51.5 1.0 N C:TYR179 4.8 34.6 1.0 CD2 C:HIS103 5.0 42.3 1.0

Iron binding site 7 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:46.9 occ:0.42 OE1 D:GLU225 2.1 53.4 1.0 NE2 D:HIS70 2.5 49.4 1.0 OD2 D:ASP107 2.7 54.0 1.0 OD1 D:ASP107 2.7 61.1 1.0 CG D:ASP107 3.0 54.4 1.0 CD D:GLU225 3.3 50.7 1.0 CE1 D:HIS70 3.4 49.6 1.0 FE D:FE302 3.5 42.4 1.0 CD2 D:HIS70 3.6 45.2 1.0 O D:SER177 3.8 37.3 1.0 OE2 D:GLU225 3.9 53.6 1.0 NE2 D:HIS103 4.0 45.9 1.0 CD2 D:HIS103 4.0 42.8 1.0 O D:HOH409 4.2 39.8 1.0 CG D:GLU225 4.5 45.6 1.0 CD2 D:LEU113 4.5 40.4 1.0 CB D:ASP107 4.5 47.1 1.0 ND1 D:HIS70 4.6 45.0 1.0 CL D:CL303 4.6 54.0 1.0 C D:SER177 4.6 38.2 1.0 OG D:SER177 4.7 52.1 1.0 CG D:HIS70 4.7 41.3 1.0 NE2 D:HIS71 4.7 49.0 1.0 CA D:GLY178 4.9 39.0 1.0

Iron binding site 8 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:42.4 occ:1.00 NE2 D:HIS71 2.1 49.0 1.0 NE2 D:HIS221 2.2 32.6 1.0 OE2 D:GLU225 2.3 53.6 1.0 CD D:GLU225 2.8 50.7 1.0 OE1 D:GLU225 2.9 53.4 1.0 CE1 D:HIS221 3.0 33.3 1.0 CL D:CL303 3.0 54.0 1.0 CE1 D:HIS71 3.1 48.4 1.0 CD2 D:HIS71 3.2 47.4 1.0 CD2 D:HIS221 3.3 33.5 1.0 FE D:FE301 3.5 46.9 0.4 ND1 D:HIS221 4.2 35.5 1.0 ND1 D:HIS71 4.2 45.0 1.0 CG D:GLU225 4.2 45.6 1.0 CD2 D:HIS70 4.3 45.2 1.0 CA D:GLY178 4.3 39.0 1.0 CG D:HIS71 4.3 43.7 1.0 CG D:HIS221 4.3 33.7 1.0 NE2 D:HIS70 4.3 49.4 1.0 NE2 D:HIS103 4.4 45.9 1.0 CE1 B:HIS204 4.5 54.0 1.0 NE2 B:HIS204 4.6 51.5 1.0 N D:TYR179 4.8 38.8 1.0 CD2 D:HIS103 5.0 42.8 1.0

Iron binding site 9 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:72.4 occ:0.62 OE2 E:GLU225 2.1 51.5 1.0 OD1 E:ASP107 2.5 57.7 1.0 OD2 E:ASP107 2.7 54.1 1.0 NE2 E:HIS70 2.7 44.2 1.0 CG E:ASP107 2.9 55.6 1.0 CD E:GLU225 3.4 45.1 1.0 O E:HOH401 3.4 46.5 1.0 O E:SER177 3.6 46.0 1.0 CE1 E:HIS70 3.6 42.0 1.0 FE E:FE302 3.7 46.1 1.0 CD2 E:HIS70 3.8 38.9 1.0 O E:HOH408 3.9 43.3 1.0 OE1 E:GLU225 4.0 45.9 1.0 NE2 E:HIS103 4.2 48.0 1.0 CD2 E:HIS103 4.2 44.4 1.0 CB E:ASP107 4.3 54.9 1.0 OG E:SER177 4.4 53.5 1.0 C E:SER177 4.4 40.6 1.0 CD1 E:LEU113 4.4 36.1 1.0 CG E:GLU225 4.4 42.0 1.0 CL E:CL303 4.7 48.0 1.0 CA E:GLY178 4.7 39.5 1.0 ND1 E:HIS70 4.8 37.8 1.0 CG E:HIS70 4.9 37.2 1.0 N E:GLY178 5.0 36.7 1.0

Iron binding site 10 out of 12 in the Oxidized Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Oxidized Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe302 b:46.1 occ:1.00 NE2 E:HIS71 2.1 54.5 1.0 NE2 E:HIS221 2.1 42.0 1.0 OE1 E:GLU225 2.3 45.9 1.0 CE1 E:HIS221 2.9 40.2 1.0 CL E:CL303 2.9 48.0 1.0 CD E:GLU225 3.0 45.1 1.0 OE2 E:GLU225 3.0 51.5 1.0 CE1 E:HIS71 3.0 52.4 1.0 CD2 E:HIS71 3.1 50.9 1.0 CD2 E:HIS221 3.2 41.5 1.0 FE E:FE301 3.7 72.4 0.6 O E:HOH401 4.0 46.5 1.0 ND1 E:HIS221 4.1 39.1 1.0 ND1 E:HIS71 4.2 50.4 1.0 CG E:HIS71 4.2 45.4 1.0 NE2 E:HIS103 4.2 48.0 1.0 CG E:HIS221 4.3 40.5 1.0 CA E:GLY178 4.3 39.5 1.0 CD2 E:HIS70 4.3 38.9 1.0 CG E:GLU225 4.4 42.0 1.0 NE2 C:HIS204 4.4 54.8 1.0 NE2 E:HIS70 4.4 44.2 1.0 CE1 C:HIS204 4.5 57.6 1.0 N E:TYR179 4.7 39.0 1.0 CD2 E:HIS103 4.9 44.4 1.0

T.Fujishiro, U.Ermler, S.Shima. A Possible Iron Delivery Function of the Dinuclear Iron Center of Hcgd in [Fe]-Hydrogenase Cofactor Biosynthesis Febs Lett. V. 588 2789 2014.
ISSN: ISSN 0014-5793
PubMed: 24931373
DOI: 10.1016/J.FEBSLET.2014.05.059